Variant report

Variant	rs1251573
Chromosome Location	chr1:76562921-76562922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10493582	0.86[CHB][hapmap]
rs10493583	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873866	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1251568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1251569	0.86[CHB][hapmap]
rs1251570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1251574	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1335738	0.81[JPT][hapmap]
rs17660966	0.86[CHB][hapmap]
rs289688	0.81[JPT][hapmap]
rs289691	0.81[JPT][hapmap]
rs427589	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1251573	ST6GALNAC3	cis	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76542800-76572000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:76548400-76576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:76557400-76605800	Weak transcription	Fetal Intestine Small	intestine
4	chr1:76557600-76588800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:76559600-76566800	Weak transcription	Fetal Lung	lung
6	chr1:76560000-76571000	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:76560200-76573400	Weak transcription	Brain Angular Gyrus	brain
8	chr1:76561800-76569200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:76561800-76572000	Weak transcription	Brain Anterior Caudate	brain
10	chr1:76562000-76563200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:76562000-76566400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:76562200-76571400	Weak transcription	Fetal Kidney	kidney
13	chr1:76562800-76563400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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